| |
Name | Pathway Name /
Pathway No. | Accession
Type | Initial
Conc.
(uM) | Volume
(fL) | Buffered | Sum Total Of |
| 21 | CaEPump | CaRegulation
Pathway No. 86 | Network | 0.005 | 1000 | No | - |
| | The calcium electrogenic pump. See McBurney and Neering 1987 TINS 10(4):164-169 We treat the pump as a simple Michaelis-Menten enzyme. Levels are constrained tightly by the need to keep resting Ca levels at about 80 nM. |
| 22 | CaM | CaM
Pathway No. 81 | Network | 20 | 1000 | No | - |
| | There is a LOT of this in the cell: upto 1% of total protein mass. (Alberts et al, Mol Biol. of the Cell, Garland Publishers) Say 25 uM. Meyer et al Science 256 1199-1202 1992 refer to studies saying it is comparable to CaMK levels. |
| 23 | CaM(Ca)n-CaNAB | Shared_Object_
Synaptic_
Network
Pathway No. 70Network | 0 | 1000 | No | CaMCa4-CaNAB
CaMCa3-CaNAB
CaMCa2-CANAB
| |
| | This pool sums the levels of the CaM.Ca2.CaNAB, CaM.Ca3.CaNAB and CaM.Ca4.CaNAB pools. |
| 24 | CaM-Ca3 | Shared_Object_
Synaptic_
Network
Pathway No. 70Network | 0 | 1000 | No | - | |
| | The TR1 end now begins to bind Ca. This form has 2 Ca's on the TR2 end, and one on the TR1. |
| 25 | CaM-Ca4 | Shared_Object_
Synaptic_
Network
Pathway No. 70Network | 0 | 1000 | No | - | |
| | The four-calcium-bound form of CaM. It is the active form for most reactions. |
| 26 | CaM-GEF | Ras
Pathway No. 76 | Network | 0 | 1000 | No | - |
| | See Farnsworth et al Nature 376 524-527 1995 |
| 27 | CaM-TR2-Ca2 | Shared_Object_
Synaptic_
Network
Pathway No. 70Network | 0 | 1000 | No | - | |
| | This is the intermediate where the TR2 end (the high-affinity end) has bound the Ca but the TR1 end has not. |
| 28 | CaM.PDE1 | AC
Pathway No. 85 | Network | 0 | 1000 | No | - |
| | PDE1 is the 66 KDa form which binds CaM. Borisy et al J Neurosci 12(3):915-923 report a 6x stimulation with calcium. |
| 29 | CaMCa2-CANAB | PP2B
Pathway No. 83 | Network | 0 | 1000 | No | - |
| | Ca2.CaM.Ca4.CaNAB The CaM has only 2 calciums attached, but CaNAB has all 4. This contributes equally to enzyme activity along with the Ca3 and Ca4 forms. |
| 30 | CaMCa3-CaNAB | PP2B
Pathway No. 83 | Network | 0 | 1000 | No | - |
| | Ca3.CaM.Ca4.CaNAB This is assumed to have the same enzymatic activity as the other Ca states of CaM bound to CaNAB. Hence I just put this into a summation with the other states and utilize the sum for the enzymatic steps. |
| 31 | CaMCa4-CaNAB | PP2B
Pathway No. 83 | Network | 0 | 1000 | No | - |
| | Ca4.CaM.Ca4.CaNAB. This form is fullly loaded with Ca. Its activity is assumed to be the same as the lower Ca-bound forms of CaM.Ca4.CaNAB. |
| 32 | CaMK-thr306 | CaMKII
Pathway No. 80 | Network | 0 | 1000 | No | - |
| | This forms due to basal autophosphorylation, but I think it has to be considered as a pathway even if some CaM is floating around. In either case it will tend to block further binding of CaM, and will not display any enzyme activity. See Hanson and Schulman JBC 267:24 pp17216-17224 1992 |
| 33 | CaMKII | CaMKII
Pathway No. 80 | Network | 70 | 1000 | No | - |
| | Huge concentration of CaMKII. In PSD it is 20-40% of protein, so we assume it is around 2.5% of protein in spine as a whole. This level is so high it is unlikely to matter much if we are off a bit. This comes to about 70 uM. Seen the review: Hanson and Schulman 1992 Ann. Rev. Biuochem 60:559-601 |
| 34 | CaMKII*** | CaMKII
Pathway No. 80 | Network | 0 | 1000 | No | - |
| | From Hanson and Schulman, the CaMKII does a lot of autophosphorylation just after the CaM is released. This prevents further CaM binding and renders the enzyme quite independent of Ca. |
| 35 | CaMKII-CaM | CaMKII
Pathway No. 80 | Network | 0 | 1000 | No | - |
| | This is the regular, CaM-activated form of CaMKII. See the review Hanson and Schulman 1992 Ann. Rev. Biochem 60:559-601 |
| 36 | CaMKII-thr286 | CaMKII
Pathway No. 80 | Network | 0 | 1000 | No | - |
| | The threonine-286 phosphorylated form of CaMKII. It is likely to be a short-lived intermediate, since it will be phosphorylated further as soon as the CAM falls off. |
| 37 | CaMKII-thr286*-C
aM | CaMKII
Pathway No. 80 | Network | 0 | 1000 | No | - |
| | From Hanson and Schulman, the thr286 is responsible for autonomous activation of CaMKII. |
| 38 | cAMP | Shared_Object_
Synaptic_
Network
Pathway No. 70Network | 0 | 1000 | No | - | | 39 | cAMP-PDE | AC
Pathway No. 85 | Network | 0.45 | 1000 | No | - | | | The levels of the PDE are not known at this time. However, enough kinetic info and info about steady-state levels of cAMP etc are around to make it possible to estimate this. | | 40 | cAMP-PDE* | AC
Pathway No. 85 | Network | 0 | 1000 | No | - | | | This form has about 2X activity as plain PDE. See Sette et al JBC 269:28 18271-18274 1994. | |
arrow indicates that ordering is done according to ascending or descending order.
and 
color.